EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes

Abstract

EzEditor is a Java-based molecular sequence editor allowing manipulation of both DNA and protein sequence alignments for phylogenetic analysis. It has multiple features optimized to connect initial computer-generated multiple alignment and subsequent phylogenetic analysis by providing manual editing with reference to biological information specific to the genes under consideration. It provides various functionalities for editing rRNA alignments using secondary structure information. In addition, it supports simultaneous editing of both DNA sequences and their translated protein sequences for protein-coding genes. EzEditor is, to our knowledge, the first sequence editing software designed for both rRNA-and protein-coding genes with the visualization of biologically relevant information and should be useful in molecular phylogenetic studies. EzEditor is based on Java, can be run on all major computer operating systems and is freely available from http://sw.ezbiocloud.net/ezeditor/.

Humibacter soli sp. nov., isolated from soil

“…Sequence alignment and similarity calculation based on almost complete 16S rRNA gene sequences between strain R1-20 T and other species of the genus Humibacter were carried out by using EzEditor (Jeon et al, 2014) and EzTaxon (Kim et al, 2012). A phylogenetic tree was inferred using the Jukes-Cantor model (Jukes & Cantor, 1969) and neighbour-joining algorithm (Saitou & Nei, 1987) with MEGA 6.0 (Tamura et al, 2013).…”

A report on 33 unrecorded bacterial species of Korea isolated in 2014, belonging to the class Gammaproteobacteria

“…The cutoff vale of 98.5% sequence similarity was applied for the identification of species. For phylogenetic analyses, multiple alignments between the 16S rRNA gene sequences of the isolates and those of the valid type strains were carried out using the ClustalW program and manually checked with the EzEditor (Jeon et al, 2014). Based on the sequences aligned, phylogenetic trees were generated by using neighbor-joining method (Saitou and Nei, 1987) that is programmed in MEGA 6.0 software (Tamura et al, 2013).…”

First Report on Characterization of Citrus Disease Causing Bacteria and Related Phages Isolated in Pakistan

“…The sequenced fragment of 16S rRNA gene assembled and edited using EzEditor software (Jeon et al, 2014) the genetic similarity of the strains was determined using EzTaxon server (http://www.ezbiocloud.net/eztaxon) (Kim et al, 2012) and the Neighbor-joining phylogenetic tree was generated using MEGA-6 (Tamura et al, 2013).…”